.TH g_rdf 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
.SH NAME
g_rdf - calculates radial distribution functions

.B VERSION 4.5
.SH SYNOPSIS
\f3g_rdf\fP
.BI "\-f" " traj.xtc "
.BI "\-s" " topol.tpr "
.BI "\-n" " index.ndx "
.BI "\-d" " sfactor.dat "
.BI "\-o" " rdf.xvg "
.BI "\-sq" " sq.xvg "
.BI "\-cn" " rdf_cn.xvg "
.BI "\-hq" " hq.xvg "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-bin" " real "
.BI "\-[no]com" ""
.BI "\-surf" " enum "
.BI "\-rdf" " enum "
.BI "\-[no]pbc" ""
.BI "\-[no]norm" ""
.BI "\-[no]xy" ""
.BI "\-cut" " real "
.BI "\-ng" " int "
.BI "\-fade" " real "
.BI "\-nlevel" " int "
.BI "\-startq" " real "
.BI "\-endq" " real "
.BI "\-energy" " real "
.SH DESCRIPTION
\&The structure of liquids can be studied by either neutron or X\-ray
\&scattering. The most common way to describe liquid structure is by a
\&radial distribution function. However, this is not easy to obtain from
\&a scattering experiment.


\&g_rdf calculates radial distribution functions in different ways.
\&The normal method is around a (set of) particle(s), the other methods
\&are around the center of mass of a set of particles (\fB \-com\fR)
\&or to the closest particle in a set (\fB \-surf\fR).
\&With all methods rdf's can also be calculated around axes parallel
\&to the z\-axis with option \fB \-xy\fR.
\&With option \fB \-surf\fR normalization can not be used.


\&The option \fB \-rdf\fR sets the type of rdf to be computed.
\&Default is for atoms or particles, but one can also select center
\&of mass or geometry of molecules or residues. In all cases only
\&the atoms in the index groups are taken into account.
\&For molecules and/or the center of mass option a run input file
\&is required.
\&Other weighting than COM or COG can currently only be achieved
\&by providing a run input file with different masses.
\&Options \fB \-com\fR and \fB \-surf\fR also work in conjunction
\&with \fB \-rdf\fR.


\&If a run input file is supplied (\fB \-s\fR) and \fB \-rdf\fR is set
\&to \fB atom\fR, exclusions defined
\&in that file are taken into account when calculating the rdf.
\&The option \fB \-cut\fR is meant as an alternative way to avoid
\&intramolecular peaks in the rdf plot.
\&It is however better to supply a run input file with a higher number of
\&exclusions. For eg. benzene a topology with nrexcl set to 5
\&would eliminate all intramolecular contributions to the rdf.
\&Note that all atoms in the selected groups are used, also the ones
\&that don't have Lennard\-Jones interactions.


\&Option \fB \-cn\fR produces the cumulative number rdf,
\&i.e. the average number of particles within a distance r.


\&To bridge the gap between theory and experiment structure factors can
\&be computed (option \fB \-sq\fR). The algorithm uses FFT, the grid
\&spacing of which is determined by option \fB \-grid\fR.
.SH FILES
.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-s" " topol.tpr" 
.B Input, Opt.
 Structure+mass(db): tpr tpb tpa gro g96 pdb 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-d" " sfactor.dat" 
.B Input, Opt.
 Generic data file 

.BI "\-o" " rdf.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-sq" " sq.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-cn" " rdf_cn.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-hq" " hq.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-[no]w"  "no    "
 View output xvg, xpm, eps and pdb files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-bin"  " real" " 0.002 " 
 Binwidth (nm)

.BI "\-[no]com"  "no    "
 RDF with respect to the center of mass of first group

.BI "\-surf"  " enum" " no" 
 RDF with respect to the surface of the first group: \fB no\fR, \fB mol\fR or \fB res\fR

.BI "\-rdf"  " enum" " atom" 
 RDF type: \fB atom\fR, \fB mol_com\fR, \fB mol_cog\fR, \fB res_com\fR or \fB res_cog\fR

.BI "\-[no]pbc"  "yes   "
 Use periodic boundary conditions for computing distances. Without PBC the maximum range will be three times the largest box edge.

.BI "\-[no]norm"  "yes   "
 Normalize for volume and density

.BI "\-[no]xy"  "no    "
 Use only the x and y components of the distance

.BI "\-cut"  " real" " 0     " 
 Shortest distance (nm) to be considered

.BI "\-ng"  " int" " 1" 
 Number of secondary groups to compute RDFs around a central group

.BI "\-fade"  " real" " 0     " 
 From this distance onwards the RDF is tranformed by g'(r) = 1 + [g(r)\-1] exp(\-(r/fade\-1)2 to make it go to 1 smoothly. If fade is 0.0 nothing is done.

.BI "\-nlevel"  " int" " 20" 
 Number of different colors in the diffraction image

.BI "\-startq"  " real" " 0     " 
 Starting q (1/nm) 

.BI "\-endq"  " real" " 60    " 
 Ending q (1/nm)

.BI "\-energy"  " real" " 12    " 
 Energy of the incoming X\-ray (keV) 

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
